Escherichia coli K-12 substr. MG1655 Polypeptide: probable TonB-dependent receptor

Gene: yncD Accession Numbers: G6762 (EcoCyc), b1451, ECK1445

Regulation Summary Diagram: ?

Regulation summary diagram for yncD

YncD is an uncharacterized protein. Sequence similarity suggests that it is an outer membrane receptor involved with iron transport is a member of the Outer Membrane Receptor (OMR) family [Zhai02].

Locations: outer membrane

Map Position: [1,518,987 <- 1,521,089] (32.74 centisomes, 118°)
Length: 2103 bp / 700 aa

Molecular Weight of Polypeptide: 77.261 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0004839 , DIP:DIP-12750N , EchoBASE:EB3536 , EcoGene:EG13774 , EcoliWiki:b1451 , ModBase:P76115 , OU-Microarray:b1451 , PortEco:yncD , Pride:P76115 , Protein Model Portal:P76115 , RefSeq:NP_415968 , RegulonDB:G6762 , SMR:P76115 , String:511145.b1451 , UniProt:P76115

Relationship Links: InterPro:IN-FAMILY:IPR000531 , InterPro:IN-FAMILY:IPR010105 , InterPro:IN-FAMILY:IPR012910 , Pfam:IN-FAMILY:PF00593 , Pfam:IN-FAMILY:PF07715 , Prosite:IN-FAMILY:PS00430 , Prosite:IN-FAMILY:PS01156

In Paralogous Gene Group: 51 (8 members)

GO Terms:

Biological Process: GO:0006810 - transport Inferred by computational analysis [GOA01a]
GO:0015891 - siderophore transport Inferred by computational analysis [GOA01a]
Molecular Function: GO:0004872 - receptor activity Inferred by computational analysis [GOA01a]
GO:0005506 - iron ion binding Inferred by computational analysis [GOA01a]
Cellular Component: GO:0009279 - cell outer membrane Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, DiazMejia09]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11a]

MultiFun Terms: transport Channel-type Transporters Beta barrel porins (The Outer Membrane Porin (OMP) Functional Superfamily)

Essentiality data for yncD knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Sequence Features

Protein sequence of probable TonB-dependent receptor with features indicated

Feature Class Location Citations Comment
Signal-Sequence 1 -> 23
UniProt: Non-Experimental Qualifier: potential;
Chain 24 -> 700
UniProt: Probable tonB-dependent receptor yncD;
Protein-Segment 680 -> 700
UniProt: TonB C-terminal box; Sequence Annotation Type: short sequence motif.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Zhai02: Zhai Y, Saier MH (2002). "The beta-barrel finder (BBF) program, allowing identification of outer membrane beta-barrel proteins encoded within prokaryotic genomes." Protein Sci 11(9);2196-207. PMID: 12192075

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Thu Oct 8, 2015, biocyc11.